SmartDock: Artificial Intelligence for Drug Discovery

13th June 2017

We are happy to introduce SmartDock, a prototype system to discriminate binders and non-binders from docking results based on Artificial Intelligence. The pharmacologic impact of drugs depends on their ability to engage and occupy physiologically relevant target receptor binding sites. However, this binding is not static but dynamic and the pharmacologic action is determined by the temporal stability of the drug-target complex. Very often, drug-target residence time is directly linked to the ability of the drug...

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VET in bioinformatics, a good way to attract young talent

14th December 2016

Vocational Education and Training (commonly known as VET) in bioinformatics is sure to be a way for many young people to enter the job market and a good gateway to companies in the healthcare and life sciences sector looking to add junior technicians to their teams, not just PhDs. Our sector is growing in Catalonia, as are the companies that are moving past the start-up phase to become professional organisations with multidisciplinary teams. At Mind the Byte, established in 2011, we are a team of 10 professionals, mainly...

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Computational drug discovery for safer drugs

3rd February 2016

Some weeks ago six people were hospitalized (one dead) after receiving a trial treatment of a new drug (BIA-10-2474), they were participating in a clinical trial. Some researchers have questioned the design of this fatal clinical trial. Ignoring the fact of a possible mistake on the trial design and, although there is an important lack of information, it is possible that the fatal result of the trial is due to off target. It means, the candidate molecule binds an unexpected target. We are not experts on clinical trials and we will not...

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Intrinsically Disordered Proteins (IDPs) and Drug Discovery

25th January 2016

Intrinsically Disordered Proteins (IDPs) are an emerging family of proteins whose which characteristic feature is that they don't present a folded structure, and thus challenge the sequence-structure-function paradigm. This lack of stable structure, over the entire protein length or in some regions, provides them a structural plasticity, that is not achievable by ordered proteins, essential to carry out their cellular function. IDPs represents the 40% of the human proteome, and play key roles in a wide range of cellular processes, being...

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The five truths of Synthetic Biology: A collaboration between Mind the Byte and ASBTEC

1st October 2015

Collaboration with non-profit entities is very precious for a company values. In Mind the Byte, we think that that kind of activities are very helpful for us in many senses. That is why we have collaborated with the Catalan Association of Biotechnologists (ASBTEC, because of the Catalan acronym) to come up with the workshop "The five truths of Synthetic Biology". This is a very specific course about fundamentals and applications of Synthetic Biology. ASBTEC is a local non-profit entity that promotes specific courses in life sciences...

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Molecular Dynamics simulations (II)

5th May 2015

To start a simulation experimental data, such as a crystallographic structure or an NMR ensemble, or a theoretical model is required. From them the atomic coordinates are extracted and the initial velocities are assigned. The assignment is usually based on the Maxwell-Boltzmann distribution at a given temperature. Equilibration and production phase Once the initial velocities are assigned the system is equilibrated until start the data collection phase. The equilibration is important to ensure that the kinetic energy (atomic...

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Molecular Dynamics simulations (I)

8th April 2015

Molecular Dynamics (MD) integrates the Newton's laws of motion, constructing trajectories that allow to describe the temporal evolution of the positions and velocities of the particles of a given system. Assuming the ergodic hypothesis, that postulates that an average of the value of a given property over time is equivalent to the average over all configurations defining the corresponding statistical- thermodynamical ensemble, we could extract thermodynamic information of the system, i.e., the macroscopic properties of the system. The simulations...

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Protein Dynamics

25th March 2015

Proteins are flexible entities, and thus move. Its function is closely related to flexibility. To carry out any function is necessary a movement that implies a conformational change. To understand the protein function and being able to interact with it (something really important in scientific fields like Computational Drug discovery), requires the understanding of protein motions. The fluctuations between the different proteic configurations can be classified according to the length-scale, the time-scale and the amplitude and directionality...

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